Tracking bacterial lineages in complex and dynamic environments with applications for growth control and persistence

As bacteria transition from exponential to stationary phase, they change substantially in size, morphology, growth and expression profiles. These responses also vary between individual cells, but it has proved difficult to track cell lineages along the growth curve to determine the progression of events or correlations between how individual cells enter and exit dormancy. Here, we developed a platform for tracking more than 10⁵ parallel cell lineages in dense and changing cultures, independently validating that the imaged cells closely track batch populations. Initial applications show that for both Escherichia coli and Bacillus subtilis, growth changes from an 'adder' mode in exponential phase to mixed 'adder-timers' entering stationary phase, and then a near-perfect 'sizer' upon exit-creating broadly distributed cell sizes in stationary phase but rapidly returning to narrowly distributed sizes upon exit. Furthermore, cells that undergo more divisions when entering stationary phase suffer reduced survival after long periods of dormancy but are the only cells observed that persist following antibiotic treatment.